data_1DZE # _model_server_result.job_id V9MWLSbiH79kR6j5tj6O-A _model_server_result.datetime_utc '2024-11-18 00:23:43' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1dze # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":280}' # _entry.id 1DZE # _exptl.entry_id 1DZE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 885.179 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 1DZE _cell.length_a 102.4 _cell.length_b 102.4 _cell.length_c 112.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DZE _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.2 88.681001 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.4 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 GAL MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC A 400 GLC 2 n B MAN 2 B 2 MAN A 410 MAN 2 n B GAL 3 B 3 GAL A 420 GAL # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 216 A LYS 216 1_555 C C15 RET . A RET 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 GAL . B GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C46 H94 O11 P2 -2' _chem_comp.formula_weight 885.179 _chem_comp.id L3P _chem_comp.mon_nstd_flag . _chem_comp.name "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 L3P sing 458 n n C1 O1 L3P sing 459 n n C1 H12 L3P sing 460 n n C1 H11 L3P sing 461 n n C2 C3 L3P sing 462 n n C2 O2 L3P sing 463 n n C2 H2 L3P sing 464 n n C3 O3 L3P sing 465 n n C3 H32 L3P sing 466 n n C3 H31 L3P sing 467 n n C4 C5 L3P sing 468 n n C4 O4 L3P sing 469 n n C4 H42 L3P sing 470 n n C4 H41 L3P sing 471 n n C5 C6 L3P sing 472 n n C5 O5 L3P sing 473 n n C5 H5 L3P sing 474 n n C6 O6 L3P sing 475 n n C6 H62 L3P sing 476 n n C6 H61 L3P sing 477 n n O1 C11 L3P sing 478 n n O2 C41 L3P sing 479 n n O3 P1 L3P sing 480 n n O4 P1 L3P sing 481 n n O5 H5O L3P sing 482 n n O6 P2 L3P sing 483 n n O1P P1 L3P doub 484 n n O2P P1 L3P sing 485 n n O4P P2 L3P doub 486 n n O5P P2 L3P sing 487 n n O6P P2 L3P sing 488 n n O6P HOP6 L3P sing 489 n n C11 C12 L3P sing 490 n n C11 H112 L3P sing 491 n n C11 H111 L3P sing 492 n n C12 C13 L3P sing 493 n n C12 H122 L3P sing 494 n n C12 H121 L3P sing 495 n n C13 C14 L3P sing 496 n n C13 C15 L3P sing 497 n n C13 H13 L3P sing 498 n n C14 H143 L3P sing 499 n n C14 H142 L3P sing 500 n n C14 H141 L3P sing 501 n n C15 C16 L3P sing 502 n n C15 H152 L3P sing 503 n n C15 H151 L3P sing 504 n n C16 C17 L3P sing 505 n n C16 H162 L3P sing 506 n n C16 H161 L3P sing 507 n n C17 C18 L3P sing 508 n n C17 H172 L3P sing 509 n n C17 H171 L3P sing 510 n n C18 C19 L3P sing 511 n n C18 C20 L3P sing 512 n n C18 H18 L3P sing 513 n n C19 H193 L3P sing 514 n n C19 H192 L3P sing 515 n n C19 H191 L3P sing 516 n n C20 C21 L3P sing 517 n n C20 H202 L3P sing 518 n n C20 H201 L3P sing 519 n n C21 C22 L3P sing 520 n n C21 H212 L3P sing 521 n n C21 H211 L3P sing 522 n n C22 C23 L3P sing 523 n n C22 H222 L3P sing 524 n n C22 H221 L3P sing 525 n n C23 C24 L3P sing 526 n n C23 C25 L3P sing 527 n n C23 H23 L3P sing 528 n n C24 H243 L3P sing 529 n n C24 H242 L3P sing 530 n n C24 H241 L3P sing 531 n n C25 C26 L3P sing 532 n n C25 H252 L3P sing 533 n n C25 H251 L3P sing 534 n n C26 C27 L3P sing 535 n n C26 H262 L3P sing 536 n n C26 H261 L3P sing 537 n n C27 C28 L3P sing 538 n n C27 H272 L3P sing 539 n n C27 H271 L3P sing 540 n n C28 C29 L3P sing 541 n n C28 C30 L3P sing 542 n n C28 H28 L3P sing 543 n n C29 H293 L3P sing 544 n n C29 H292 L3P sing 545 n n C29 H291 L3P sing 546 n n C30 H303 L3P sing 547 n n C30 H302 L3P sing 548 n n C30 H301 L3P sing 549 n n C41 C42 L3P sing 550 n n C41 H412 L3P sing 551 n n C41 H411 L3P sing 552 n n C42 C43 L3P sing 553 n n C42 H422 L3P sing 554 n n C42 H421 L3P sing 555 n n C43 C44 L3P sing 556 n n C43 C45 L3P sing 557 n n C43 H43 L3P sing 558 n n C44 H443 L3P sing 559 n n C44 H442 L3P sing 560 n n C44 H441 L3P sing 561 n n C45 C46 L3P sing 562 n n C45 H452 L3P sing 563 n n C45 H451 L3P sing 564 n n C46 C47 L3P sing 565 n n C46 H462 L3P sing 566 n n C46 H461 L3P sing 567 n n C47 C48 L3P sing 568 n n C47 H472 L3P sing 569 n n C47 H471 L3P sing 570 n n C48 C49 L3P sing 571 n n C48 C50 L3P sing 572 n n C48 H48 L3P sing 573 n n C49 H493 L3P sing 574 n n C49 H492 L3P sing 575 n n C49 H491 L3P sing 576 n n C50 C51 L3P sing 577 n n C50 H502 L3P sing 578 n n C50 H501 L3P sing 579 n n C51 C52 L3P sing 580 n n C51 H512 L3P sing 581 n n C51 H511 L3P sing 582 n n C52 C53 L3P sing 583 n n C52 H522 L3P sing 584 n n C52 H521 L3P sing 585 n n C53 C54 L3P sing 586 n n C53 C55 L3P sing 587 n n C53 H53 L3P sing 588 n n C54 H543 L3P sing 589 n n C54 H542 L3P sing 590 n n C54 H541 L3P sing 591 n n C55 C56 L3P sing 592 n n C55 H552 L3P sing 593 n n C55 H551 L3P sing 594 n n C56 C57 L3P sing 595 n n C56 H562 L3P sing 596 n n C56 H561 L3P sing 597 n n C57 C58 L3P sing 598 n n C57 H572 L3P sing 599 n n C57 H571 L3P sing 600 n n C58 C59 L3P sing 601 n n C58 C60 L3P sing 602 n n C58 H58 L3P sing 603 n n C59 H593 L3P sing 604 n n C59 H592 L3P sing 605 n n C59 H591 L3P sing 606 n n C60 H603 L3P sing 607 n n C60 H602 L3P sing 608 n n C60 H601 L3P sing 609 n n # _atom_sites.entry_id 1DZE _atom_sites.fract_transf_matrix[1][1] 0.009766 _atom_sites.fract_transf_matrix[1][2] 0.005638 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011276 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008905 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 RET A 1 250 250 RET RET . D 4 L1P A 1 260 260 L1P L1P . E 5 L2P A 1 270 270 L2P L2P . F 6 L3P A 1 280 280 L3P L3P . G 7 L4P A 1 290 290 L4P L4P . H 5 L2P A 1 300 300 L2P L2P . I 8 HOH A 1 2001 2001 HOH HOH . I 8 HOH A 2 2002 2002 HOH HOH . I 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH A 4 2004 2004 HOH HOH . I 8 HOH A 5 2005 2005 HOH HOH . I 8 HOH A 6 2006 2006 HOH HOH . I 8 HOH A 7 2007 2007 HOH HOH . I 8 HOH A 8 2008 2008 HOH HOH . I 8 HOH A 9 2009 2009 HOH HOH . I 8 HOH A 10 2010 2010 HOH HOH . I 8 HOH A 11 2011 2011 HOH HOH . I 8 HOH A 12 2012 2012 HOH HOH . I 8 HOH A 13 2013 2013 HOH HOH . I 8 HOH A 14 2014 2014 HOH HOH . I 8 HOH A 15 2015 2015 HOH HOH . I 8 HOH A 16 2016 2016 HOH HOH . I 8 HOH A 17 2017 2017 HOH HOH . I 8 HOH A 18 2018 2018 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 L3P . . . F 6 28.62 39.309 13.692 1 89.13 ? C1 L3P 280 A 1 HETATM 2 C C2 L3P . . . F 6 28.504 39.913 12.279 1 90.63 ? C2 L3P 280 A 1 HETATM 3 C C3 L3P . . . F 6 28.857 38.872 11.18 1 93.57 ? C3 L3P 280 A 1 HETATM 4 C C4 L3P . . . F 6 29.633 35.348 8.482 1 100 ? C4 L3P 280 A 1 HETATM 5 C C5 L3P . . . F 6 30.995 35.573 7.819 1 100 ? C5 L3P 280 A 1 HETATM 6 C C6 L3P . . . F 6 31.928 34.37 7.978 1 100 ? C6 L3P 280 A 1 HETATM 7 O O1 L3P . . . F 6 28.61 40.356 14.687 1 82.08 ? O1 L3P 280 A 1 HETATM 8 O O2 L3P . . . F 6 27.194 40.474 12.073 1 95.02 ? O2 L3P 280 A 1 HETATM 9 O O3 L3P . . . F 6 27.903 37.793 11.135 1 100 ? O3 L3P 280 A 1 HETATM 10 O O4 L3P . . . F 6 29.354 36.475 9.334 1 100 ? O4 L3P 280 A 1 HETATM 11 O O5 L3P . . . F 6 30.843 35.902 6.437 1 100 ? O5 L3P 280 A 1 HETATM 12 O O6 L3P . . . F 6 31.258 33.106 7.956 1 100 ? O6 L3P 280 A 1 HETATM 13 O O1P L3P . . . F 6 27.063 37.403 8.784 1 100 ? O1P L3P 280 A 1 HETATM 14 O O2P L3P . . . F 6 27.221 35.499 10.288 1 100 ? O2P L3P 280 A 1 HETATM 15 O O4P L3P . . . F 6 33.147 31.889 6.834 1 100 ? O4P L3P 280 A 1 HETATM 16 O O5P L3P . . . F 6 33.009 31.851 9.239 1 100 ? O5P L3P 280 A 1 HETATM 17 O O6P L3P . . . F 6 31.44 30.568 7.925 1 100 ? O6P L3P 280 A 1 HETATM 18 P P1 L3P . . . F 6 27.856 36.775 9.869 1 100 ? P1 L3P 280 A 1 HETATM 19 P P2 L3P . . . F 6 32.222 31.819 7.988 1 100 ? P2 L3P 280 A 1 HETATM 20 C C11 L3P . . . F 6 28.942 40.045 16.057 1 90.72 ? C11 L3P 280 A 1 HETATM 21 C C12 L3P . . . F 6 28.75 41.282 16.957 1 91.05 ? C12 L3P 280 A 1 HETATM 22 C C13 L3P . . . F 6 29.483 41.096 18.305 1 88.1 ? C13 L3P 280 A 1 HETATM 23 C C14 L3P . . . F 6 28.893 39.899 19.057 1 88.22 ? C14 L3P 280 A 1 HETATM 24 C C15 L3P . . . F 6 29.287 42.36 19.153 1 88.51 ? C15 L3P 280 A 1 HETATM 25 C C16 L3P . . . F 6 30.094 42.273 20.454 1 87.32 ? C16 L3P 280 A 1 HETATM 26 C C17 L3P . . . F 6 30.124 43.663 21.099 1 85.39 ? C17 L3P 280 A 1 HETATM 27 C C18 L3P . . . F 6 31.288 43.761 22.088 1 82.42 ? C18 L3P 280 A 1 HETATM 28 C C19 L3P . . . F 6 30.745 43.616 23.515 1 85.47 ? C19 L3P 280 A 1 HETATM 29 C C20 L3P . . . F 6 31.964 45.13 21.925 1 80.88 ? C20 L3P 280 A 1 HETATM 30 C C21 L3P . . . F 6 32.775 45.473 23.179 1 78.77 ? C21 L3P 280 A 1 HETATM 31 C C41 L3P . . . F 6 26.019 39.646 12.065 1 98 ? C41 L3P 280 A 1 HETATM 32 C C42 L3P . . . F 6 25.425 39.554 13.477 1 95.88 ? C42 L3P 280 A 1 HETATM 33 C C43 L3P . . . F 6 24.578 38.28 13.594 1 91.24 ? C43 L3P 280 A 1 HETATM 34 C C44 L3P . . . F 6 23.487 38.288 12.52 1 92.05 ? C44 L3P 280 A 1 HETATM 35 C C45 L3P . . . F 6 23.916 38.242 14.969 1 88.47 ? C45 L3P 280 A 1 HETATM 36 C C46 L3P . . . F 6 24.767 37.392 15.908 1 88.34 ? C46 L3P 280 A 1 HETATM 37 C C47 L3P . . . F 6 24.449 37.778 17.351 1 85.95 ? C47 L3P 280 A 1 HETATM 38 C C48 L3P . . . F 6 25.665 37.487 18.226 1 85.02 ? C48 L3P 280 A 1 HETATM 39 C C49 L3P . . . F 6 25.44 36.175 18.964 1 82.74 ? C49 L3P 280 A 1 HETATM 40 C C50 L3P . . . F 6 25.835 38.614 19.244 1 87.33 ? C50 L3P 280 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 40 #